Links

From Fiji

• Fiji's Google+ page
• ImageJ's Google+ page
• ImageJ
• ImageJ User Manual
• ImageJ Documentation Wiki
• ImageJDev, a project to advance the core of ImageJ, also hosting our nightly Jenkins build
• About the relationship between ImageJDev (also known as ImageJ2) and Fiji
• Wikipedia page on ImageJ
• Wikipedia page on Fiji
• Fiji on OHLOH
• ObjectJ

Links to the contributors' personal pages can be found here.

Contents 1 More ImageJ plugins 2 Image Processing and Ethics 3 Input/Output 3.1 Movie support 4 Image Processing 5 Programming in science 6 Java 7 Miscellaneous 8 Imaging Networks and Facilities

More ImageJ plugins

• Plugins on the ImageJ website, specifically links to external websites
• Plugins on the ImageJ Documentation Wiki
• The Biomedical Imaging Group in Lausanne has many interesting plugins.
• Christian Henden has some interesting plugins (mainly in the Public Domain), including 3D threshold methods: http://www.pvv.org/~perchrh/imagej/

Image Processing and Ethics

It becomes more and more important to have clear-cut guidelines what types of image processing are appropriate and what processing is questionable at best.

Here is a comprehensive list of 12 rules you need to follow if you want to perform science rather than art.

Input/Output

Movie support

There is a beta-quality Movie support for all of Fiji's supported platforms available via the update site http://pacific.mpi-cbg.de/~schindelin/ffmpeg-plugins/ (see these instructions on how to follow an update site).

Bio-Formats has started supporting parts of the Quicktime specification without relying on the native Quicktime4Java that is not even supported on 64-bit MacOSX, let alone Linux.

Image Processing

A pixel is not a little square. Really. It is not. Pixels may be spaced on a regular grid. But that does not make them square. Even thinking about them as squares will harm your analysis, since it is simply wrong.

Explore the Hypermedia Image Processing Reference of the Department of Artificial Intelligence in the University of Edinburgh for an extensive overview of available image processing techniques.

The University of Edinburgh also has the rather complete CVonline compendium of Computer Vision.

A scientific image is not a photograph!

External tutorials.

Programming in science

In research Software should be treated just like materials: if you publish your results, you should publish the software (including source code), too.

Even Nature says that your code is good enough; you should publish it if you want to be a good scientist.

If you're still unsure and think that your code is not good enough, then publish it under a license appropriate for science.

Java

• An introduction to Java for kids (ebook)
• Mixing light-weight (Swing) and heavy-weight (AWT) components

• A generics tutorial

• Infrequently Asked Questions about Java

Miscellaneous

• An explanation where ImageJ's icon's microscope comes from.

Imaging Networks and Facilities

• Imaging Facility Network (Dresden Biopolis)